Methods and compositions relating to microbial treatment and diagnosis of disorders

Abstract

The present disclosure provides methods, systems, compositions, and kits to address the need for microbiome-related treatment of health conditions and disease. The present disclosure provides for treatment of metabolic conditions using microbial compositions.

What is claimed is: 
     
       1. A composition comprising:
   Akkermansia muciniphila , wherein the  Akkermansia muciniphila  has been cultured in a culture medium comprising substantially a plant-based culture medium. 
 
     
     
       2. The composition of  claim 1 , wherein the composition is of an oral dosage form, wherein the oral dosage form is a pill, tablet, capsule, or liquid capsule. 
     
     
       3. The oral dosage form of  claim 2 , wherein the oral dosage form is a food, a drink, a dietary supplement, or a pharmaceutical formulation. 
     
     
       4. The oral dosage form of  claim 2 , wherein the oral dosage form is a bar, a chewable form, a gummy, or a suspension. 
     
     
       5. The composition of  claim 1 , wherein the composition further comprises a vitamin. 
     
     
       6. The composition of  claim 1 , wherein the composition further comprises a prebiotic. 
     
     
       7. The composition of  claim 6 , wherein the prebiotic is selected from the group consisting of an amino acid, a peptide, biotin, polydextrose, a fructooligosaccharide (FOS), a galactooligosaccharide (GOS), a mannan oligosaccharide (MOS), a xylooligosaccharide (XOS), inulin, lignin, psyllium, chitin, chitosan, a gum, high amylose cornstarch (HAS), a β-glucan, lactulose, oligofructose-enriched inulin, oligofructose, oligodextrose, tagatose, trans-galactooligosaccharide, pectin, and a combination thereof. 
     
     
       8. The composition of  claim 1 , further comprising a pharmaceutically-acceptable excipient. 
     
     
       9. The composition of  claim 1 , further comprising one or more carriers or excipients selected from the group consisting of a lipid, a protein, a polypeptide, an amino acid, an antioxidant, a metal or mineral, an oil, dextrose, glycerol, a flavoring agent, a sweetening agent, a coloring agent, a detakifier, a tonicity adjusting agent, a surfactant, and an emulsifying agent. 
     
     
       10. The composition of  claim 1 , wherein the composition further comprises a stabilizing agent that enhances stability and/or survival of the  Akkermansia muciniphila.    
     
     
       11. The composition of  claim 1 , wherein the composition has a shelf life of at least about 1 month. 
     
     
       12. The composition of  claim 1 , wherein the composition has a shelf life of at least about 1 month when stored at a temperature of about 20° C., 22° C., or 25° C. 
     
     
       13. The composition of  claim 1 , wherein the composition further comprises at least one enteric coating or at least one preservative. 
     
     
       14. The composition of  claim 1 , further comprising at least one microbe comprising an rRNA sequence with at least about 97% sequence identity to an rRNA sequence from a microbe selected from the group consisting  Anaerostipes caccae, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium longum, Butyrivibrio fibrisolvens, Clostridium acetobutylicum, Clostridium aminophilum, Clostridium beijerinckii, Clostridium butyricum, Clostridium colinum, Clostridium indolis, Clostridium orbiscindens, Enterococcus faecium, Eubacterium hallii, Eubacterium rectale, Faecalibacterium prausnitzii, Fibrobacter succinogenes, Lactobacillus acidophilus, Lactobacillus brevis, Lactobacillus bulgaricus, Lactobacillus casei, Lactobacillus caucasicus, Lactobacillus fermentum, Lactobacillus helveticus, Lactobacillus lactis, Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus rhamnosus, Oscillospira guilliermondii, Roseburia cecicola, Roseburia inulinivorans, Ruminococcus flavefaciens, Ruminococcus gnavus, Ruminococcus obeum, Streptococcus cremoris, Streptococcus faecium, Streptococcus infantis, Streptococcus mutans, Streptococcus thermophilus, Anaerofustis stercorihominis, Anaerostipes hadrus, Anaerotruncus colihominis, Clostridium sporogenes, Clostridium tetani, Coprococcus eutactus, Eubacterium cylindroides, Eubacterium dolichum, Eubacterium ventriosum, Roseburia faeccis, Roseburia hominis, Roseburia intestinalis , and any combination thereof. 
     
     
       15. The composition of  claim 1 , further comprising a microbe with an rRNA sequence with at least about 97% sequence identity to a 16s rRNA sequence of  Eubacterium hallii.    
     
     
       16. The composition of  claim 1 , wherein the  Akkermansia muciniphila  is a lyophilized  Akkermansia muciniphila.    
     
     
       17. The composition of  claim 1 , wherein the composition comprises at least about 10{circumflex over ( )}6 colony forming units (CFU) of the cultured  Akkermansia muciniphila.    
     
     
       18. The composition of  claim 1 , wherein the plant-based culture medium comprises yeast extract, a plant-derived peptone, a plant-derived hydrolysate, or a combination thereof.